SG: Will phylogenomics resolve the most difficult parts of the tree of life: an empirical evaluation with the turtle genus Pseudemys

物种是科学研究、保护和管理的最重要的生物单位。作为一个社会，我们根据《濒危物种法》保护物种，我们观察、狩猎和欣赏原生栖息地的物种，我们管理国家公园进行物种保护。随着新的分子技术和工具的出现，研究人员现在可以使用整个基因组，包括数十亿条信息，以几年前不可想象的方式精确确定一个分类群或地理区域中出现了多少物种。随着这些信息量极大的数据集的出现，那些研究物种和物种形成的人目前面临着两难境地：收集什么数据，以及如何分析这些数据，以便能够快速、准确、廉价地识别和划定所有生命的物种。在这个项目中，研究小组将评估目前正在使用的三种最有希望的、最先进的方法，以确定哪种基因组方法对来自美国东南部的一群淡水海龟的物种鉴定和划界是最佳的。尽管这一类群分布广泛，并在生态学上得到了很好的研究，但几十年来一直阻碍着准确的物种划分；它还包含两个极度濒危的类群。这个项目的工作将为寻求利用基因组数据识别、划定和保护物种的生物学家提供重要的指导。在这项分析中，海龟属被用作一个极其困难的群体的经验例子，以确定物种的界定和相互关系。该项目使用比较基因组学方法，对假眼小鼠内所有九个潜在分类群进行广泛采样，以评估三种基因组方法的相对有效性和威力：限制位点相关DNA(RADseq)、靶向浓缩，即使用从现有基因组资源设计的探针对基因组的已知部分进行测序，以及低覆盖率的全基因组重测序。一种新的比较方法被用来询问这些数据流中的哪一种基于成本、实验室工作的简易性和效率以及经验表现而表现最佳。在这样做的过程中，将解决系统学中的两个基本问题。首先，利用大量的基因组数据来确定谱系，以及为极其困难的群体重建物种树的前景如何？第二，考虑到目前可用于生成和分析基因组数据的方法，什么方法是最优的？总体而言，该项目的结果将为困难群体的分析提供一般指导方针，并明确解决美国东南部一个重要的动物群组成部分的实证案例研究。

Species are the most important biological unit of scientific research, conservation and management. As a society, we protect species under the Endangered Species Act, we observe, hunt, and admire species in their native habitats, and we manage national parks for species conservation. As new molecular technologies and tools have become available, researchers can now use the entire genome, including billions of pieces of information, to precisely determine how many species occur in a taxonomic group or geographical region in ways that were inconceivable a few years ago. As these extremely informative data sets become available, those who study species and speciation are currently facing the dilemma of what data to collect and how to analyze those data so that species can be quickly, accurately, and inexpensively identified and delimited across all of life. In this project, the research team will evaluate the three most promising, cutting edge approaches that are currently in use to determine which genomic method is optimal for species identification and delimitation in a group of freshwater turtles from the southeastern United States. This group, although widespread and well studied ecologically, has thwarted accurate species delimitation for decades; it also contains two critically endangered taxa. The work in this project will provide critical guidance for the large group of biologists who seek to identify, delimit, and protect species using genomic data.In this analysis, the turtle genus Pseudemys is used as an empirical example of an extremely difficult group to determine species delimitation and interrelationships. The project uses a comparative genomic approach with extensive rangewide sampling of all nine potential taxa within Pseudemys to evaluate the relative efficacy and power of three genomic approaches: restriction-site associated DNA (RADseq), targeted enrichment where known portions of the genome are sequenced using probes designed from existing genomic resources, and low-coverage, whole genome resequencing. A novel comparative approach is utilized to ask which of these data streams performs optimally based on cost, ease and efficiency of lab work, and empirical performance. In so doing, two fundamental issues in systematics will be addressed. First, what are the prospects for identifying lineages, and for reconstructing species trees for extremely difficult groups using large amounts of genomic data? And second, given the current methods available for generating and analyzing genomic data, what approach is optimal? Overall, the results of this project will provide both general guidelines for analyses of difficult groups and clear resolution of this empirical case study of an important faunal component of the southeastern United States.